Another data point: the key binding for Undo (Shift-Command-Z) exhibits similar behavior, i.e. it is executed twice.  And trying with Python 2.7.1 linked with A/S Tk 8.5 and with the old key bindings where Shift-Command-S is Save Copy rather than Save As, it appears that now two Save Copy events happen.  So it appears to happen in general (?) when Shift is combined with another accelerator. But it doesn't happen with Option-Command-S in 3.2.  And, using the Wish 8.5 menu demo, I was not able to reproduce the problem there by simply changing the accelerators to from Command-<letter> to Shift-Command-<letter>.  So it's hard not to rule out something in IDLE yet.